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I came across this gene Pepc (peptidase C)

NCBI gene database has a page for it here https://www.ncbi.nlm.nih.gov/gene/109616

But it does not contain any information on its coding sequence or genomic location. It just says it sits on chromosome 1.

Can someone familiar with how the reference genome is annotated explain why this is?

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  • $\begingroup$ I agree that this is an odd gene: no transcript, but it has mouse strains and supporting literature. $\endgroup$
    – gringer
    Jul 9, 2023 at 20:18
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    $\begingroup$ I like the question a lot. You can't have this sitting on arguably (sure EBI would disagree) the worlds most comprehensive molecular database, not as comprehensive as it thinks it is. This is one for escalation with NCBI and the authors. If this was EBML Emily would step in. Definitely upvoted, I would recommend site members upvote to help the OP recover their bounty costs. I am aware this sort of thing goes on ... I've encountered in a completely different area. $\endgroup$
    – M__
    Jul 14, 2023 at 16:57
  • $\begingroup$ Let me know if you intend to escalate it, because I will otherwise. $\endgroup$
    – M__
    Jul 14, 2023 at 17:27
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    $\begingroup$ @M__ Thanks for the comment. I'm not sure what you mean by escalating. Do you mean reaching out directly to NCBI? $\endgroup$
    – geom_na
    Jul 15, 2023 at 17:05
  • $\begingroup$ Yes, you can approach the authors but it never results in success (I've tried - not on this example). $\endgroup$
    – M__
    Jul 15, 2023 at 17:43

1 Answer 1

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This gene/protein appears to have been described exclusively as an isozyme / electrophoretic mobility assay of a protein.

See for example this PepC mutant page:

The Pepc locus controls electrophoretic mobility of the enzyme peptidase C of red blood cells. This LT/J congenic strain carries the Pepca allele from C57BL/6 that determines a slow anodally migrating electrophoretic band.

The relevant publications describing mutants are from the 70s and 80s, e.g. here, when there were no genomic resources for mice.

However, linkage mapping of electrophoretic variants could be used to establish linkage to loci on chromosome 1, apparently.

Very likely PepC is encoded by some annotated gene on chr1, but no one knows which one exactly because they don't really know much about the protein other than its electrophoretic variability. But that's just a guess by me.

When the databases were set up, they had to accommodate 1) mouse mutant strains, and 2) published articles referencing the protein, so they did their best.

However, no one ever followed up to link everything together, so we just have these orphan entries.

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